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JBrowse PSB 2020

Wed, 07/31/2019 - 18:46

Created page with "==Overview== In this workshop, we present an introduction to the JBrowse genome browser using a preconfigured VirtualBox appliance that attendees will be able to use with th..."

New page

==Overview==

In this workshop, we present an introduction to the JBrowse genome browser using a preconfigured VirtualBox appliance that attendees will be able to use with their own computers to participate. We will cover installing and configuring JBrowse for a variety of common data formats including FASTA, GFF3, BAM, BigWig, VCF, and CRAM. We will also cover setting up JBrowse Connect, a server-side component for integrating computational analysis resources such as Galaxy into your JBrowse instance, and review new features such as the Apollo genome curation tool, the human genome data release, and JBrowse 2, which will see its first official release shortly before the workshop.

===Relevance to PSB===

The JBrowse JavaScript genome browser is a very widely used genome browser, deployed at thousands of sites with around 30,000 monthly active users (source: Google Analytics). JBrowse can be deployed as a “static site” (i.e. no server CPU usage beyond delivering static files to the client), on cheap or cloud storage (including e.g. from an Amazon S3 bucket), making it the ideal secure and cost-efficient mode of presenting results of high-throughput genome analyses, for personalized genome medicine, and for many other applications in computational genomics. The Apollo genome annotation editor allows community and/or crowdsourced curation of gene structures and feature annotations over the web. The features of JBrowse being published in 2019 (including a new version of Apollo, the JBrowse 2 codebase which fundamentally pushes bioinformatics analysis into the browser, the integration with Galaxy, and other features) are highly relevant as visualization and analysis front-ends to bioinformatics researchers, and a natural fit to trainees, graduate students, postdocs, and industry attendees of the PSB conference.

====Tutorial Level ====

Beginner to Intermediate. Students should be comfortable performing simple command line tasks like moving files and running scripts.

====Intended Audience====

JBrowse is sufficiently easy to install that a biologist, bioinformatics researcher, or bioinformatics developer can easily set up and configure a JBrowse server after the initial hurdles of learning about configuration options and file formats are overcome. This talk is intended to help them over those hurdles and to introduce the more advanced features of JBrowse, the preconfigured datasets and auxiliary applications like JBrowse Connect, and the features coming in JBrowse 2.

====Prerequisite Software and VirtualBox Images ====

Prerequisite software for JBrowse will be pre-installed on VirtualBox images on USB drives that will be distributed to workshop attendees. Participants using these VirtualBox images will be able to setup and configure JBrowse during the workshop.

After the workshop, a VirtualBox system image with JBrowse prerequisite software pre-installed will be made available on JBrowse tutorial page at GMOD.org [[JBrowse#Tutorials]]. Users will be able to use this image to walk through the material presented at this workshop.

===Workshop Schedule ===
Times based on 9am-10:30am time slot.
{| class="wikitable"
|-
!Time
!Presenter
!Topic
|-
|9am-9:10am
|Ian Holmes
|Welcome, JBrowse overview
|-
|9:10am-9:25am
|Rob Buels
|JBrowse 2: A component architecture for building genome browser apps
|-
|9:25am-10:00am
|Scott Cain
|JBrowse setup and usage tutorial
|-
|10:00am-10:15am
|Ian Holmes
|JBrowse, Apollo, and Galaxy: beyond browsing to interactive editing
|-
|10:15am-10:30am
|Shihab Dider
|JBrowse hg38 human instance & associated data
|}

===Tutorial Summary ===

The 9:25-10:00 section of the workshop will be based on the successful JBrowse tutorial workshop presented by Scott Cain at the January 2019 Plant and Animal Genomes conference, updated and extended to include the new JBrowse features appearing throughout 2019, and streamlined reflecting the probable greater familiarity of PSB attendees with some of the basic bioinformatics issues and shorter timeframe. A detailed plan of the previously presented version of this workshop can be found at [[JBrowse_Tutorial_PAG_2019]]

Key points will include:
* Instructions on how to download, install, configure, and test a JBrowse installation
* The three basic steps: load reference sequences, index tracks, build the name index
* Overview of data sources: GFF, BED, BAM, VCF, CRAM, Wiggle/BigWig
* Overview of track types and options: SVG, Canvas, HTML, paired reads, coverage
* Changing the appearance and dynamic behavior of tracks
* Overview of the JBrowse plugin ecosystem: installing plugins, the plugin repository, notable and significant plugins
* Advanced features of the user interface: highlighting regions and features, opening local files (and the standalone JBrowse desktop app), finding set intersections and unions using “combination tracks”

===Connecting to Galaxy ===
This part of the workshop will describe the JBrowse Connect platform for initiating and managing tasks through the JBrowse UI, and will walk through the specific example of proxying a Galaxy BLAST workflow into the JBrowse app, so that users can BLAST data against the reference genome.

===JBrowse 2 ===

JBrowse 2 is a radical redesign of JBrowse from the ground up, preserving the capabilities of JBrowse (especially the ability to interface with many data sources) but moving to a more modular architecture and a React-style model where the rendered DOM is a function of application state. Many new features are available in JBrowse 2 and this part of the workshop will introduce them for the first time.

===JBrowse Human Instance ===

JBrowse is increasingly used by labs working in cancer genomics to visualize variants including structural variants such as gene fusions. JBrowse 2 will include new UI features to visualize these. The JBrowse team has assembled a reference instance of human genome data that can be used for human genome analyses, encompassing data from Ensembl, ENCODE, UCSC, the 1000 genomes project, COSMIC, and other sources. This part of the workshop will include a tour of this data bundle, with a guide to deploying it for human-centered applications in biomedicine, especially cancer research.

[[Category:JBrowse]]
[[Category:Conferences]]
[[Category:GMOD_Component]]
[[Category:Tutorial]] Scott
Categories: Bio

Public Chado Databases

Tue, 06/25/2019 - 10:56

‎FlyBase

← Older revision Revision as of 14:56, 25 June 2019 Line 15: Line 15:  == Direct [[Chado]] Access == == Direct [[Chado]] Access ==  === [http://flybase.org FlyBase] === === [http://flybase.org FlyBase] === −The following connection information is for the FlyBase Chado database.  The database release available through this access point will always match the version available through our public web interface.  Before each release there will be a down time of several hours while the new data is loaded.     −'''hostname:''' chado.flybase.org<br />+* [https://flybase.github.io/docs/chado/index#public-database FlyBase public chado database] −'''port:''' 5432<br />+ −'''username:''' flybase<br />+ −'''password:''' no password<br />+ −'''database name:''' flybase<br />+ − + −e.g.+ − psql -h chado.flybase.org -U flybase flybase+     === [http://www.genedb.org GeneDB] === === [http://www.genedb.org GeneDB] === Jogoodma
Categories: Bio

Template:MailingListsGalaxy

Sat, 06/08/2019 - 15:26

Drooped some lists. Updated links to others.

← Older revision Revision as of 19:26, 8 June 2019 Line 3: Line 3:  | [http://announce.list.galaxyproject.org/ galaxy-announce] | [http://announce.list.galaxyproject.org/ galaxy-announce]  | Announcements of interest to the [[Galaxy]] community.  ''Low volume and moderated.'' | Announcements of interest to the [[Galaxy]] community.  ''Low volume and moderated.'' −| [http://announce.list.galaxyproject.org/ Nabble], [https://lists.galaxyproject.org/pipermail/galaxy-announce/ Mailman]+| [http://announce.list.galaxyproject.org/ Nabble], [https://lists.galaxyproject.org/archives/list/galaxy-announce@lists.galaxyproject.org/ Mailman]  |- |-  | [https://help.galaxyproject.org/ Galaxy Help] | [https://help.galaxyproject.org/ Galaxy Help] Line 10: Line 10:  |- |-  | [http://dev.list.galaxyproject.org/ galaxy-dev] | [http://dev.list.galaxyproject.org/ galaxy-dev] −| Discussion and questions regarding local installations and development of [[Galaxy]].  ''High volume.''+| Discussion and questions regarding local installations and development of [[Galaxy]].  ''Medium volume.'' −| [http://dev.list.galaxyproject.org/ Nabble], [https://lists.galaxyproject.org/pipermail/galaxy-dev/ Mailman]+| [http://dev.list.galaxyproject.org/ Nabble], [https://lists.galaxyproject.org/archives/list/galaxy-dev@lists.galaxyproject.org/ Mailman] −|-+ −| [http://Proteomics.list.galaxyproject.org/ galaxy-proteomics]+ −| General questions and discussion regarding proteomics in [[Galaxy]].  ''Low volume.''+ −| [http://protomics.list.galaxyproject.org/ Nabble], [https://lists.galaxyproject.org/pipermail/galaxy-proteomics/ Mailman]+ −|-+ −| [http://france.list.galaxyproject.org/ galaxy-france]+ −| Cette liste est destinée à l'information (et aux discussions) de la Communauté francaise Galaxy. (This list is for announcements to (and discussion within) the French Galaxy Community. Most list content is in French.) ''Faible volume / Low volume.''+ −| [http://france.list.galaxyproject.org/ Nabble]+ −|-+ −| [https://lists.galaxyproject.org/listinfo/galaxy-commits galaxy-commits]+ −| Galaxy source control commit messages.+ −| [https://lists.galaxyproject.org/pipermail/galaxy-commits/ Mailman]+ Clements
Categories: Bio

Gbol

Thu, 05/30/2019 - 08:52

← Older revision Revision as of 12:52, 30 May 2019 (2 intermediate revisions by the same user not shown)Line 1: Line 1:  This is a scratch page for thoughts on development of the GMOD Bio Object Layer (GBOL). This is a scratch page for thoughts on development of the GMOD Bio Object Layer (GBOL).  +  +  +'''== Note: This project is no longer active. ==  +'''  +  +     __TOC__ __TOC__    −==Random==  −First things first. Can we pronounce GBOL gobble?   ==Object Layer Design Goals== ==Object Layer Design Goals==  * Provide a simple object layer for manipulating generic genomic features, their locations, annotation properties, and supporting analyses. This object layer will essentially mimic the structure of GMOD's Chado schema. * Provide a simple object layer for manipulating generic genomic features, their locations, annotation properties, and supporting analyses. This object layer will essentially mimic the structure of GMOD's Chado schema. Line 133: Line 137:  Is there a controlled vocabulary for annotation properties? We need to specify conventions for things like, storing feature comments and comment properties. How about annotation evidence structure and confidence codes from GO? Is there a controlled vocabulary for annotation properties? We need to specify conventions for things like, storing feature comments and comment properties. How about annotation evidence structure and confidence codes from GO?    −[[Category:GMOD Developers]]+[[Category:GMOD_Developers]]  [[Category:Proposals]] [[Category:Proposals]] Nathandunn
Categories: Bio

User:Scott

Mon, 05/20/2019 - 14:40

← Older revision Revision as of 18:40, 20 May 2019 Line 1: Line 1:  GMOD Coordinator, software development manager at [http://oicr.on.ca/ The Ontario Institute for Cancer Research]. GMOD Coordinator, software development manager at [http://oicr.on.ca/ The Ontario Institute for Cancer Research].    −Scott graduated from The Ohio State University in 1990 with a B. S. in Chemical Engineering and continued on to the University of California in San Diego for graduate school, where he studied improvements to monoclonal antibody production in industrial processes through cell culture and cell cycle modifications.  Upon earning his Ph. D. in Chemical Engineering, he began work in the software industry, working for MSI/Accelrys, Pangea Systems/DoubleTwist, and Athersys, until finally coming to rest at Cold Spring Harbor Laboratory in [[User:Lstein|Lincoln Stein's]] lab.  He is the coordinator and a lead developer of the [[Main_Page|GMOD project]], focusing mainly on core schema and tool development, but is also a developer for GBrowse as well as in the BioPerl project. Scott also teaches programming, web development and database design courses at the University of Phoenix.  Scott is a happy husband and father of fourteen year old boy-girl twins.+Scott graduated from The Ohio State University in 1990 with a B. S. in Chemical Engineering and continued on to the University of California in San Diego for graduate school, where he studied improvements to monoclonal antibody production in industrial processes through cell culture and cell cycle modifications.  Upon earning his Ph. D. in Chemical Engineering, he began work in the software industry, working for MSI/Accelrys, Pangea Systems/DoubleTwist, and Athersys, until finally coming to rest at Cold Spring Harbor Laboratory in [[User:Lstein|Lincoln Stein's]] lab, following Lincoln to [http://oicr.on.ca/ OICR] several years ago.  He is the coordinator and a lead developer of the [[Main_Page|GMOD project]], focusing mainly on core schema and tool development, but is also a developer for [http://wormbase.org/ WormBase] and the [http://alliancegenome.org/ Alliance for Genome Resources].  Scott is a happy husband and father of nineteen year old boy-girl twins.    −Scott can be reached at his email address: [http://mailhide.recaptcha.net/d?k=010I5vtKiZqC1kdmtqmWRRhg==&amp;c=6uiWfNokHIbewa_qGkyAF8Tt0sdX6xy0-BIUTsIkwlA=  sco...]@scottcain.net or Skype to username scottcain.+Scott can be reached at his email address: [http://mailhide.recaptcha.net/d?k=010I5vtKiZqC1kdmtqmWRRhg==&amp;c=6uiWfNokHIbewa_qGkyAF8Tt0sdX6xy0-BIUTsIkwlA=  sco...]@scottcain.net or Twitter @scottjcain.     [[Image:100 5955 1.jpg]] [[Image:100 5955 1.jpg]]       − +<!--  ===Publications=== ===Publications===  <ref name=PMID:18570664/> <ref name=PMID:18570664/> Line 18: Line 18:  <ref name=PMID:9041112/> <ref name=PMID:9041112/>  <references/> <references/> − +--> − + −==Support letter templates==+ − + −The [[JBrowse]] project is applying for a grant renewal from NHGRI to continue the work that JBRowse, and as part of the grant, to fund the "GMOD help desk" (that is, the stuff I do: workshops, meetings and [[Chado]] development).  The title of that grant is "Enhancements to the GMOD suite of genome annotation and visualization tools".+ − + −We need to demonstrate that we support the community and have the support of the community, and we would like to demonstrate that by submitting many letters of support from users. We would be very grateful if you could take a couple of minutes to write such a letter; it should include information about how you use or plan to use GMOD software. There are some template paragraphs below for inspiration.+ − + −The letters should be on institutional letterhead, signed, and then scanned to a PDF. Please [mailto:help@gmod.org contact the GMOD helpdesk] or [mailto:scott@scottcain.net email Scott directly] if you're willing to write a letter or if you need any help.+ − + −'''The deadline for getting the letters of support is February 28'''. + − + −This grant would help to secure the future of important parts of the GMOD project, so we would be very grateful for your help!+ − + − + −===Generic intro paragraph===+ − + −The GMOD project has two related aims: to provide open source and interoperable visualization, annotation and data management software for use with genomics data, and to foster the growth of a community of developers and users who ask diverse questions but share common problems.  The project does this in multiple ways:  they provide venues for in person interaction, including GMOD community meetings, workshops at conferences and courses, as well as avenues for online interaction, including software repositories, mailing lists, standards and a wiki-powered web site.  Their continued work is important for the future of genomics-driven biology research.+ − + −===Took a summer school course===+ − + −The GMOD projects has provided many courses to reach out to the community and get new users.  I took one of the "summer school" courses '''''WHEN, WHERE''''' which covered several topics, including Chado, JBrowse, GBrowse, Galaxy, Apollo, and Intermine.  The course brought together experts in each of the software projects (typically the lead developer) to teach and it provided an excellent opportunity both to learn about the software and to interact with both the developers and the other students who were also grappling with their own massive data influxes.+ − + −'''''More about your personal experience with the course...'''''+ − + −===Related project===+ − + −The GMOD project aims to promote communication between software communities and interoperability between software.  They provide several venues for communicating: community meetings, workshops, mailing lists, and a wiki-powered website.  They also provide some standards for software interoperability.  These are important to us '''''because ....'''''+ Scott
Categories: Bio